Genomic characterization of dryland adaptation in endangered Anxi cattle in China.

Local species exhibit distinctive indigenous characteristics while showing unique productive and phenotypic traits. However, the advent of commercialization has posed a substantial threat to the survival of indigenous species. Anxi cattle, an endangered native breed in China, have evolved unique growth and reproductive characteristics in extreme desert and semidesert ecosystems. In this study, we conducted a genomic comparison of 10 Anxi cattle genomes with those of five other global populations/breeds to assess genetic diversity and identify candidate genomic regions in Anxi cattle. Population structure and genetic diversity analyses revealed that Anxi cattle are part of the East Asian cattle clade, exhibiting higher genetic diversity than commercial breeds. Through selective sweep analysis, we identified specific genetic variations linked to the environmental adaptability of Anxi cattle. Notably, we identified several candidate genes, including CERS3 involved in regulating skin permeability and antimicrobial functions, RBFOX2 associated with cardiac development, SLC16A7 participated in the regulation of pancreatic endocrine function, and SPATA3 related to reproduction. Our findings revealed the distinctive genomic features of Anxi cattle in dryland environments, provided invaluable insights for further research and breed preservation, and had important significance for enriching the domestic cattle breeding gene bank.

Temperature adaptation patterns in Chinese cattle revealed by TRPM2 gene mutation analysis.

Cattle are sensitive to temperature fluctuations but adapt well to inclement weather conditions. When environmental temperatures exceed specific thresholds, heat stress becomes a critical concern for cattle. The TRPM2 gene, which resides on cattle chromosome 1 encodes a TRP channel protein, holding a unique capacity to sense temperature changes and facilitate rapid response to avoid heat stress. Here, we utilized the Bovine Genome Variation Database (BGVD) (http://animal.omics.pro/code/index.php/BosVar), and identified a missense mutation site, c.805A > G: p. Met269Val (rs527146862), within the TRPM2 gene. To elucidate the functional assessment of this mutation in temperature adaptation attributes of Chinese cattle, we genotyped 407 samples from 20 distinct breeds representing diverse climatic zones across China. The association analysis incorporates three temperature parameters and revealed compelling insights in terms of allele frequency. Interestingly, the prevalence of the wild-type allele A was notably higher among northern cattle breeds and this trend diminished gradually as observed in southern cattle populations. Conversely, the mutant-type allele G demonstrated a contrasting trend. Moreover, southern cattle exhibited markedly higher frequencies of GG and GA genotypes (P < 0.01). The presence of heterozygous and homozygous mutations appears to confer an enhanced capacity for adaptation to elevated temperatures. These results provide unequivocal correlation evidence between TRPM2 genotypes (AA, GA, GG) and environmental temperature parameters and comprehend the genetic mechanisms governing temperature adaptation in cattle. This provides valuable insights for strategic breed selection across diverse climatic regions, thereby aiding livestock production amid evolving climate challenges.

The TRPM2 gene encodes TRP channel protein that helps animals in combating heat stress. Twenty Chinese local cattle breeds were genotyped, and association analysis was performed. This investigation encompasses the distribution pattern of the missense mutation locus rs527146862 of the TRPM2 gene in southern, northern, and central cattle populations. The results demonstrated a significant relationship between rs527146862 locus and temperature adaptation attributes in Chinese cattle.

Impact of STAT5A-CNVs on growth traits in Chinese beef cattle breeds.

CNVs, which are a type of structural variation, make a substantial impact on diverse characteristics in multiple species. Q-PCR and data association analysis were used for STAT5A gene copy in this study. This study aimed to investigate the copy number variation (CNV) of the STAT5A gene in seven Chinese cattle breeds, namely Qinchuan cattle, Xianan cattle, Yunling cattle, Ji'an cattle, Jiaxian Red cattle, Qaidam cattle, and Guyuan yellow cattle. Blood samples were collected for CNV typing, and the correlation between CNV type and growth traits was analyzed using SPSS 23.0 software and ANOVA. The findings revealed variations in the distribution of different copy number types among the different cattle breeds. Furthermore, association analysis demonstrated a positive impact of CNV in the STAT5A gene on cattle growth: in the JX, individuals with duplication types exhibited superior performance in terms of rump length (P < 0.05). Conversely, normal GY cattle demonstrated better body height and abdomen circumference (P < 0.05), while QD cattle exhibited a significant correlation between weight and body length with normal individuals (P < 0.05). Moreover, QC bovine duplication individuals outperformed other types, with copy number variation significantly associated with chest depth, chest width, and body length (P < 0.05). The results validate the correlation between copy number variation (CNV) of the STAT5A gene and growth characteristics in five different cattle breeds, providing a reliable benchmark for the purpose of cattle breeding.

Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China.

Altay white-headed cattle have not received enough attention for several reasons. Due to irrational breeding and selection practices, the number of pure Altay white-headed cattle has decreased significantly and the breed is now on the eve of extinction. The genomic characterization will be a crucial step towards understanding the genetic basis of productivity and adaptability to survival under native Chinese agropastoral systems; nevertheless, no attempt has been made in Altay white-headed cattle. In the current study, we compared the genomes of 20 Altay white-headed cattle to the genomes of 144 individuals in representative breeds. Population genetic diversity revealed that the nucleotide diversity of Altay white-headed cattle was less than that of indicine breeds and comparable to that of Chinese taurus cattle. Using population structure analysis, we also found that Altay white-headed cattle carried the ancestry of the European and East Asian cattle lineage. In addition, we used three different methods (F ST, θπ ratio and XP-EHH) to investigate the adaptability and white-headed phenotype of Altay white-headed cattle and compared it with Bohai black cattle. We found EPB41L5, SCG5 and KIT genes on the list of the top one percent genes, these genes might have an association with environmental adaptability and the white-headed phenotype for this breed. Our research reveals the distinctive genomic features of Altay white-headed cattle at the genome-wide level.

Polymorphism in PLIN2 gene and its association with growth traits in Chinese native cattle.

Perilipin 2 (PLIN2) is a cytosolic protein that regulates intracellular lipid storage and mobilization. However, research reports of the relationship between PLIN2 gene and growth traits in cattle are rare. Here, five novel single nucleotide polymorphisms (SNPs)（g.3036G > C, g.3964C > T, g.6458G > T, g.6555C > T and g.8231G > A）were identified within the bovine PLIN2 gene using DNA sequencing and PCR-SSCP methods in 820 individuals from four Chinese indigenous bovine breeds. Overall, five common haplotypes were identified based on the 5 SNPs, with the most common haplotypes (GCGCG) occurring at a frequency of 69.0%. In addition, The 5 novel SNPs were associated with growth traits at 6, 12, 18 and 24 months in Nanyang population, and significant associations were found in body weight and heart girth. These results suggest that PLIN2 possibly is a strong candidate gene marker for body weight in cattle breeding program.

Research on association between variants and haplotypes of TRPV1 and TRPA1 genes with growth traits in three cattle breeds.

The objective of this study was to examine the association of transient receptor potential vanilloid 1 (TRPV1) and transient receptor potential ankyrin 1 (TRPA1) genes polymorphisms with growth traits in three Chinese cattle breeds (Jiaxian red cattle, Qinchuan cattle and Luxi cattle). Through experiments we identified three single nucleotide polymorphisms (SNPs) in these three cattle breeds TRPV1 and TRPA1 genes using PCR-SSCP, (forced) PCR-RFLP methods. Three of these polymorphisms are all synonymous mutation which includes (NW_003104493.1: 30327 C > T), (NW_003104493.1: 33394 A > G) and (NW_003104493.1: 38471 G > A) are in exons. The other three polymorphisms are located at 3'UTR. Furthermore, we evaluated the haplotype frequency and the statistical analyses indicated that these SNPs of TRPV1 and TRPA1 genes were associated with bovine body height, body length, waist angle width, hucklebone width, cross ministry height, chest qingwidth (p < 0.05) and recommendation height, cannon circumference (p < 0.01) of Qingchuan cattle; body length, waist angle width (p < 0.05) of Jiaxian red cattle; body weight, Body length, cannon circumference, chest circumference (p < 0.05) and body height (p < 0.01) of Luxi cattle. Our result confirms the polymorphisms in the TRPV1 and TRPA1 genes are associated with growth traits that may be used for marker-assisted selection (MAS) in three beef breeds programs.

MiR-499 regulates myoblast proliferation and differentiation by targeting transforming growth factor ß receptor 1.

MicroRNAs (miRNAs or miRs) are small noncoding RNAs that play critical roles in muscle cell proliferation and differentiation via post-transcriptional regulation of gene expression. Here, based on our previous high-throughput sequencing results, we evaluated miRNA-499 (miR-499) functions during myoblast proliferation and differentiation. In addition, we analyzed miR-499 expression profiles and characterized the associated functional roles. MiR-499 is known to be a skeletal muscle fiber-type-associated miRNA. However, its roles in skeletal myoblast proliferation and differentiation are poorly understood. MiR-499 overexpression promoted C2C12 cell proliferation and significantly attenuated C2C12 cell myogenic differentiation. Furthermore, miR-499 inhibition enhanced C2C12 cell proliferation and suppressed C2C12 cell differentiation. Using dual-luciferase reporter assays and western blot analysis, we confirmed that miR-499 targeted transforming growth factor ß receptor 1 (TGFßR1), a known regulator of skeletal myoblast development. Additionally, our RNA interference analysis, in which TGFßR1 was downregulated, showed that TGFßR1 significantly promoted the differentiation of C2C12 cells and inhibited their proliferation.

Effects of genetic variants of the bovine WNT8A gene on nine important growth traits in beef cattle.

WNT-ß-catenin-TCF pathway is involved in carcinogenesis and foetal development. As a member of the WNT gene family, Wnt8A encodes secreted signalling proteins and responds to many biological processes.However, similar research on the effects of genetic variations of Wnt8A gene on growth traits is lacking. Therefore, in this study, polymorphisms of Wnt8A were detected in 396 animals from Chinese Qinchuan cattle using DNA pool sequencing and PCR-RFLP methods. Four novel single-nucleotide polymorphisms (SNPs) of Wnt8A gene were identified, including three mutations in introns (g.T-445C, g.G244C and g.G910A) and one in exon (g.T4922C). Additionally, we examined the associations of four SNPs with growth traits. The results revealed that SNP2 (g.G244C) was significantly associated with shoulder height, hip height, body length, hip width, and body weight (P < 0.05). SNP3 (g.G910A) also displayed notable effects on hip width (P < 0.05). Meanwhile, the haplotype combination CC-GC-GA-CC was strongly associated with heavier, taller and longer animals (P < 0.05). These results show that the Wnt8A gene may be a potential candidate gene, and the SNPs could be used as molecular markers in early marker-assisted selection in beef cattle breeding programmes.

Application of mathematical expectation (ME) strategy for detecting low frequency mutations: An example for evaluating 14-bp insertion/deletion (indel) within the bovine PRNP gene.

The detection method based on the mathematical expectation (ME) strategy is fast and accuracy for low frequency mutation screening in large samples. Previous studies have found that the 14-bp insertion/deletion (indel) variants of the 3' untranslated region (3' UTR) within bovine PRNP gene have been characterized with low frequency (≤5%) in global breeds outside China, which has not been determined in Chinese cattle breeds yet. Therefore, this study aimed to identify the 14-bp indel within PRNP gene in 5 major Chinese indigenous cattle breeds and to evaluate its associations with phenotypic traits. It was the first time to use ME strategy to detect low frequency indel polymorphisms and found that minor allele frequency was 0.038 (Qinchuan), 0.033 (Xianan), 0.013 (Nanyang), 0.003 (Jiaxian), and zero (Ji'an), respectively. Compared to the traditional detection method by which the sample was screened one by one, the reaction time by using the ME method was decreased 62.5%, 64.9%, 77.6%, 88.9% and 66.4%, respectively. In addition, the 14-bp indel was significantly associated with the growth traits in 2 cattle breeds, with the body length of Qinchuan cattle as well as the body weight and waistline of Xianan cattle. Our results have uncovered that the method based on ME strategy is rapid, reliable, and cost-effective for detecting the low frequency mutation as well as our findings provide a potential valuable theoretical basis for the marker-assisted selection (MAS) in beef cattle.

Polymorphisms of FLII implicate gene expressions and growth traits in Chinese cattle.

Flightless-1 (FLII) is essential for early embryogenesis, structural organization of indirect flight muscle and can inhibit adipocyte differentiation. We therefore aimed to identify common variations in FLII gene and to investigate their effects on cattle growth traits. By DNA sequencing and forced PCR-RFLP methods, we evaluated two synonymous mutations (rs41910826 and rs444484913) and one intron mutation (rs522737248) in four Chinese domestic breeds (n = 628). Association analysis indicated that these SNPs were associated with growth traits and gene expressions (P < 0.05). At rs41910826, individuals with TT and/or CT genotypes had some better body sizes in Jiaxian, Nanyang, and Qinchuan breeds. Consistently, among adult Qinchuan cattle muscles, quantitative real-time PCR study witnessed considerable increases of mRNA level of FLII in cattle with CT genotype. For rs444484913, TT and/or TC genotypes were significantly associated with increased body traits of Qinchuan cattle while the qPCR data showed that the TT genotype was more conducive to FLII expression in fetal muscle. At rs522737248, performances of cattle with AA genotype showed compelling superior merits in all four breeds, and allele A had an increasing tendency for the mRNA expression of PPARγ in adult adipose and FLII in fetal muscle. These findings strongly demonstrate that the three SNPs of FLII gene could be utilized as molecular markers for future assisted selection in cattle breeding program.